Starting phenix.real_space_refine on Fri Jun 20 05:48:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hcn_34659/06_2025/8hcn_34659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hcn_34659/06_2025/8hcn_34659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hcn_34659/06_2025/8hcn_34659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hcn_34659/06_2025/8hcn_34659.map" model { file = "/net/cci-nas-00/data/ceres_data/8hcn_34659/06_2025/8hcn_34659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hcn_34659/06_2025/8hcn_34659.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 14898 2.51 5 N 4158 2.21 5 O 4395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23568 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 776 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "B" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "C" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4224 Classifications: {'peptide': 566} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 537} Chain: "D" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2056 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 245} Chain: "E" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 776 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "F" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "G" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4224 Classifications: {'peptide': 566} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 537} Chain: "H" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2056 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 245} Chain: "I" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 776 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "J" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "K" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4224 Classifications: {'peptide': 566} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 537} Chain: "L" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2056 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 245} Time building chain proxies: 14.34, per 1000 atoms: 0.61 Number of scatterers: 23568 At special positions: 0 Unit cell: (149.604, 151.248, 90.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4395 8.00 N 4158 7.00 C 14898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 3.1 seconds 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5634 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 48 sheets defined 30.0% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 4 through 27 Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.616A pdb=" N VAL B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 140 through 150 removed outlier: 3.997A pdb=" N GLU C 144 " --> pdb=" O PRO C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.654A pdb=" N ALA C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 185 removed outlier: 4.257A pdb=" N TYR C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 212 removed outlier: 3.860A pdb=" N LEU C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 225 through 240 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.901A pdb=" N THR C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 320 removed outlier: 3.622A pdb=" N MET C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.806A pdb=" N ASP C 346 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 386 removed outlier: 3.522A pdb=" N ARG C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 477 through 479 No H-bonds generated for 'chain 'C' and resid 477 through 479' Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 219 through 225 removed outlier: 6.968A pdb=" N LEU D 223 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 225 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 263 Proline residue: D 259 - end of helix Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'E' and resid 4 through 27 Processing helix chain 'E' and resid 31 through 50 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 72 through 77 Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.652A pdb=" N VAL F 45 " --> pdb=" O PHE F 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 14 Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 140 through 150 removed outlier: 4.025A pdb=" N GLU G 144 " --> pdb=" O PRO G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 168 removed outlier: 3.625A pdb=" N ALA G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 removed outlier: 4.149A pdb=" N TYR G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP G 185 " --> pdb=" O LEU G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 212 removed outlier: 3.867A pdb=" N LEU G 205 " --> pdb=" O GLN G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 240 Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 282 through 290 Processing helix chain 'G' and resid 298 through 302 removed outlier: 3.901A pdb=" N THR G 301 " --> pdb=" O THR G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 320 removed outlier: 3.624A pdb=" N MET G 315 " --> pdb=" O GLU G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 333 Processing helix chain 'G' and resid 338 through 351 removed outlier: 3.828A pdb=" N ASP G 346 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL G 347 " --> pdb=" O ALA G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 386 removed outlier: 3.548A pdb=" N ARG G 373 " --> pdb=" O GLU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'G' and resid 409 through 415 Processing helix chain 'G' and resid 436 through 440 removed outlier: 3.572A pdb=" N PHE G 440 " --> pdb=" O PRO G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 479 No H-bonds generated for 'chain 'G' and resid 477 through 479' Processing helix chain 'G' and resid 480 through 487 Processing helix chain 'G' and resid 493 through 500 Processing helix chain 'G' and resid 500 through 506 Processing helix chain 'G' and resid 521 through 525 Processing helix chain 'H' and resid 207 through 218 Processing helix chain 'H' and resid 219 through 225 removed outlier: 6.972A pdb=" N LEU H 223 " --> pdb=" O PRO H 220 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR H 224 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA H 225 " --> pdb=" O GLY H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 263 Proline residue: H 259 - end of helix Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'I' and resid 4 through 27 Processing helix chain 'I' and resid 31 through 50 Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 67 through 69 No H-bonds generated for 'chain 'I' and resid 67 through 69' Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'J' and resid 41 through 45 removed outlier: 3.598A pdb=" N VAL J 45 " --> pdb=" O PHE J 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.651A pdb=" N CYS K 65 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 150 removed outlier: 4.041A pdb=" N GLU K 144 " --> pdb=" O PRO K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 168 removed outlier: 3.679A pdb=" N ALA K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 185 removed outlier: 4.126A pdb=" N TYR K 176 " --> pdb=" O PRO K 172 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP K 185 " --> pdb=" O LEU K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 212 removed outlier: 3.876A pdb=" N LEU K 205 " --> pdb=" O GLN K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 240 Processing helix chain 'K' and resid 255 through 264 Processing helix chain 'K' and resid 282 through 290 Processing helix chain 'K' and resid 298 through 302 removed outlier: 3.928A pdb=" N THR K 301 " --> pdb=" O THR K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 320 removed outlier: 3.630A pdb=" N MET K 315 " --> pdb=" O GLU K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 333 Processing helix chain 'K' and resid 338 through 351 removed outlier: 3.811A pdb=" N ASP K 346 " --> pdb=" O ILE K 342 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL K 347 " --> pdb=" O ALA K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 386 removed outlier: 3.537A pdb=" N ARG K 373 " --> pdb=" O GLU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 405 Processing helix chain 'K' and resid 409 through 415 Processing helix chain 'K' and resid 436 through 440 Processing helix chain 'K' and resid 477 through 479 No H-bonds generated for 'chain 'K' and resid 477 through 479' Processing helix chain 'K' and resid 480 through 487 Processing helix chain 'K' and resid 493 through 499 Processing helix chain 'K' and resid 500 through 505 Processing helix chain 'L' and resid 207 through 218 Processing helix chain 'L' and resid 219 through 225 removed outlier: 6.978A pdb=" N LEU L 223 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR L 224 " --> pdb=" O LEU L 221 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA L 225 " --> pdb=" O GLY L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 263 Proline residue: L 259 - end of helix Processing helix chain 'L' and resid 269 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 7.400A pdb=" N LEU A 64 " --> pdb=" O ILE A 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 86 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB1, first strand: chain 'C' and resid 34 through 35 removed outlier: 6.775A pdb=" N ASP C 34 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP C 85 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 76 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 82 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU C 74 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA C 84 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN C 72 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 69 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 97 removed outlier: 6.667A pdb=" N GLY C 87 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE C 96 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP C 85 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 76 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 82 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU C 74 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA C 84 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN C 72 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA C 128 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 447 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 136 removed outlier: 6.424A pdb=" N GLY C 130 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 155 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP C 132 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLY C 157 " --> pdb=" O ASP C 132 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N HIS C 134 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 215 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL C 243 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 268 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 492 removed outlier: 5.896A pdb=" N THR C 490 " --> pdb=" O ALA C 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 534 through 535 Processing sheet with id=AB7, first strand: chain 'D' and resid 27 through 36 removed outlier: 4.997A pdb=" N THR D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA D 24 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU D 30 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS D 22 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA D 99 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE D 131 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 101 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR D 133 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN D 103 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS D 135 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 105 " --> pdb=" O HIS D 135 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL D 172 " --> pdb=" O PRO D 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 52 through 55 removed outlier: 6.926A pdb=" N THR D 81 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU D 116 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 83 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA D 120 " --> pdb=" O CYS D 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 52 through 55 removed outlier: 6.926A pdb=" N THR D 81 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU D 116 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 83 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 64 through 65 removed outlier: 7.405A pdb=" N LEU E 64 " --> pdb=" O ILE E 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 79 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=AC4, first strand: chain 'F' and resid 34 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC7, first strand: chain 'G' and resid 29 through 31 Processing sheet with id=AC8, first strand: chain 'G' and resid 34 through 35 removed outlier: 6.784A pdb=" N ASP G 34 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ASP G 85 " --> pdb=" O ASP G 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL G 76 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL G 82 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU G 74 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA G 84 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN G 72 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL G 69 " --> pdb=" O ILE G 119 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 92 through 97 removed outlier: 5.012A pdb=" N ILE G 93 " --> pdb=" O LYS G 89 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS G 89 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL G 76 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL G 82 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU G 74 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA G 84 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN G 72 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA G 128 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL G 447 " --> pdb=" O ALA G 454 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 99 through 100 Processing sheet with id=AD2, first strand: chain 'G' and resid 130 through 136 removed outlier: 6.406A pdb=" N GLY G 130 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL G 155 " --> pdb=" O GLY G 130 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP G 132 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLY G 157 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N HIS G 134 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY G 215 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 243 " --> pdb=" O HIS G 269 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE G 268 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 489 through 492 Processing sheet with id=AD4, first strand: chain 'G' and resid 534 through 535 Processing sheet with id=AD5, first strand: chain 'H' and resid 27 through 36 removed outlier: 4.994A pdb=" N THR H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA H 24 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU H 30 " --> pdb=" O HIS H 22 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS H 22 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA H 99 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE H 131 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL H 101 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR H 133 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN H 103 " --> pdb=" O THR H 133 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS H 135 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU H 105 " --> pdb=" O HIS H 135 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL H 172 " --> pdb=" O PRO H 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 52 through 55 removed outlier: 6.930A pdb=" N THR H 81 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU H 116 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE H 83 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA H 120 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 52 through 55 removed outlier: 6.930A pdb=" N THR H 81 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU H 116 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE H 83 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 64 through 65 removed outlier: 7.434A pdb=" N LEU I 64 " --> pdb=" O ILE I 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 79 through 86 Processing sheet with id=AE1, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AE2, first strand: chain 'J' and resid 34 through 37 Processing sheet with id=AE3, first strand: chain 'J' and resid 89 through 90 Processing sheet with id=AE4, first strand: chain 'K' and resid 34 through 35 removed outlier: 6.768A pdb=" N ASP K 34 " --> pdb=" O LYS K 83 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ASP K 85 " --> pdb=" O ASP K 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY K 80 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL K 76 " --> pdb=" O GLY K 80 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL K 82 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU K 74 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA K 84 " --> pdb=" O ASN K 72 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN K 72 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL K 69 " --> pdb=" O ILE K 119 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 92 through 97 removed outlier: 6.671A pdb=" N GLY K 87 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE K 96 " --> pdb=" O ASP K 85 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP K 85 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY K 80 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL K 76 " --> pdb=" O GLY K 80 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL K 82 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU K 74 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA K 84 " --> pdb=" O ASN K 72 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN K 72 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA K 128 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL K 447 " --> pdb=" O ALA K 454 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 99 through 100 Processing sheet with id=AE7, first strand: chain 'K' and resid 130 through 136 removed outlier: 6.415A pdb=" N GLY K 130 " --> pdb=" O THR K 153 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL K 155 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP K 132 " --> pdb=" O VAL K 155 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLY K 157 " --> pdb=" O ASP K 132 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N HIS K 134 " --> pdb=" O GLY K 157 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY K 215 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL K 243 " --> pdb=" O HIS K 269 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE K 268 " --> pdb=" O LEU K 294 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 130 through 136 removed outlier: 6.415A pdb=" N GLY K 130 " --> pdb=" O THR K 153 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL K 155 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP K 132 " --> pdb=" O VAL K 155 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLY K 157 " --> pdb=" O ASP K 132 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N HIS K 134 " --> pdb=" O GLY K 157 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE K 191 " --> pdb=" O PHE K 491 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N THR K 490 " --> pdb=" O ALA K 512 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 534 through 535 Processing sheet with id=AF1, first strand: chain 'L' and resid 27 through 36 removed outlier: 4.995A pdb=" N THR L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA L 24 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU L 30 " --> pdb=" O HIS L 22 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS L 22 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA L 99 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE L 131 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL L 101 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR L 133 " --> pdb=" O VAL L 101 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN L 103 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS L 135 " --> pdb=" O GLN L 103 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU L 105 " --> pdb=" O HIS L 135 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL L 172 " --> pdb=" O PRO L 176 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 52 through 55 removed outlier: 6.944A pdb=" N THR L 81 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU L 116 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE L 83 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA L 120 " --> pdb=" O CYS L 149 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 52 through 55 removed outlier: 6.944A pdb=" N THR L 81 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU L 116 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE L 83 " --> pdb=" O LEU L 116 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2577 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.63 Time building geometry restraints manager: 7.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8017 1.34 - 1.46: 4497 1.46 - 1.57: 11375 1.57 - 1.69: 0 1.69 - 1.81: 189 Bond restraints: 24078 Sorted by residual: bond pdb=" C LYS G 443 " pdb=" O LYS G 443 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.73e+00 bond pdb=" C ASN K 299 " pdb=" N PRO K 300 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.53e-01 bond pdb=" CA ASP G 25 " pdb=" CB ASP G 25 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.53e-01 bond pdb=" C ASN G 299 " pdb=" N PRO G 300 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.46e-01 bond pdb=" CA ASP C 25 " pdb=" CB ASP C 25 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.69e-02 3.50e+03 7.26e-01 ... (remaining 24073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 32183 1.56 - 3.13: 503 3.13 - 4.69: 68 4.69 - 6.25: 24 6.25 - 7.82: 9 Bond angle restraints: 32787 Sorted by residual: angle pdb=" N THR G 467 " pdb=" CA THR G 467 " pdb=" C THR G 467 " ideal model delta sigma weight residual 109.81 117.63 -7.82 2.21e+00 2.05e-01 1.25e+01 angle pdb=" N THR K 467 " pdb=" CA THR K 467 " pdb=" C THR K 467 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N THR C 467 " pdb=" CA THR C 467 " pdb=" C THR C 467 " ideal model delta sigma weight residual 109.81 117.27 -7.46 2.21e+00 2.05e-01 1.14e+01 angle pdb=" C ALA G 24 " pdb=" N ASP G 25 " pdb=" CA ASP G 25 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C ALA C 24 " pdb=" N ASP C 25 " pdb=" CA ASP C 25 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 ... (remaining 32782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 13164 17.41 - 34.81: 994 34.81 - 52.22: 149 52.22 - 69.63: 20 69.63 - 87.03: 25 Dihedral angle restraints: 14352 sinusoidal: 5577 harmonic: 8775 Sorted by residual: dihedral pdb=" CA TRP C 435 " pdb=" C TRP C 435 " pdb=" N SER C 436 " pdb=" CA SER C 436 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP K 435 " pdb=" C TRP K 435 " pdb=" N SER K 436 " pdb=" CA SER K 436 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP G 360 " pdb=" C ASP G 360 " pdb=" N SER G 361 " pdb=" CA SER G 361 " ideal model delta harmonic sigma weight residual 180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2352 0.033 - 0.066: 919 0.066 - 0.099: 306 0.099 - 0.132: 181 0.132 - 0.165: 7 Chirality restraints: 3765 Sorted by residual: chirality pdb=" CA ASP C 25 " pdb=" N ASP C 25 " pdb=" C ASP C 25 " pdb=" CB ASP C 25 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA ASP K 25 " pdb=" N ASP K 25 " pdb=" C ASP K 25 " pdb=" CB ASP K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA ASP G 25 " pdb=" N ASP G 25 " pdb=" C ASP G 25 " pdb=" CB ASP G 25 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 3762 not shown) Planarity restraints: 4296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 145 " -0.019 2.00e-02 2.50e+03 1.72e-02 7.36e+00 pdb=" CG TRP D 145 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 145 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 145 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 145 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 145 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 145 " -0.020 2.00e-02 2.50e+03 1.70e-02 7.24e+00 pdb=" CG TRP L 145 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP L 145 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP L 145 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP L 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 145 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 145 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 145 " 0.020 2.00e-02 2.50e+03 1.70e-02 7.21e+00 pdb=" CG TRP H 145 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP H 145 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 145 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 145 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 145 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 145 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 145 " -0.001 2.00e-02 2.50e+03 ... (remaining 4293 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2424 2.75 - 3.29: 23397 3.29 - 3.82: 41712 3.82 - 4.36: 52879 4.36 - 4.90: 89843 Nonbonded interactions: 210255 Sorted by model distance: nonbonded pdb=" OG SER K 297 " pdb=" OE2 GLU K 345 " model vdw 2.209 3.040 nonbonded pdb=" OG SER G 297 " pdb=" OE2 GLU G 345 " model vdw 2.212 3.040 nonbonded pdb=" O LEU C 566 " pdb=" NH1 ARG E 23 " model vdw 2.215 3.120 nonbonded pdb=" O LEU G 566 " pdb=" NH1 ARG I 23 " model vdw 2.222 3.120 nonbonded pdb=" O PRO B 64 " pdb=" OG1 THR B 67 " model vdw 2.231 3.040 ... (remaining 210250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 57.360 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24078 Z= 0.131 Angle : 0.511 7.816 32787 Z= 0.262 Chirality : 0.044 0.165 3765 Planarity : 0.004 0.040 4296 Dihedral : 12.712 87.035 8718 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3075 helix: 1.72 (0.20), residues: 744 sheet: 0.01 (0.19), residues: 714 loop : -0.49 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 145 HIS 0.004 0.001 HIS G 415 PHE 0.007 0.001 PHE H 238 TYR 0.007 0.001 TYR D 204 ARG 0.002 0.000 ARG C 338 Details of bonding type rmsd hydrogen bonds : bond 0.14670 ( 934) hydrogen bonds : angle 7.43741 ( 2577) covalent geometry : bond 0.00297 (24078) covalent geometry : angle 0.51133 (32787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8769 (mp0) cc_final: 0.7947 (mp0) REVERT: A 45 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 31 ASP cc_start: 0.8186 (p0) cc_final: 0.7892 (p0) REVERT: B 52 ASP cc_start: 0.8708 (t0) cc_final: 0.8427 (t0) REVERT: B 55 GLN cc_start: 0.8603 (tt0) cc_final: 0.8294 (tt0) REVERT: B 78 GLU cc_start: 0.8407 (tt0) cc_final: 0.8091 (tm-30) REVERT: C 11 ASP cc_start: 0.8342 (m-30) cc_final: 0.8042 (m-30) REVERT: D 50 GLU cc_start: 0.8706 (pm20) cc_final: 0.8458 (pm20) REVERT: D 68 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 146 ASP cc_start: 0.8093 (t70) cc_final: 0.7610 (t0) REVERT: D 175 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 264 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8349 (mmtm) REVERT: E 2 GLU cc_start: 0.8710 (mp0) cc_final: 0.7701 (mp0) REVERT: E 45 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7682 (mm-30) REVERT: F 27 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7917 (mp0) REVERT: F 31 ASP cc_start: 0.8272 (p0) cc_final: 0.7936 (p0) REVERT: F 55 GLN cc_start: 0.8610 (tt0) cc_final: 0.8324 (tt0) REVERT: G 11 ASP cc_start: 0.8352 (m-30) cc_final: 0.8079 (m-30) REVERT: G 117 GLU cc_start: 0.7833 (tp30) cc_final: 0.7623 (tp30) REVERT: H 68 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7811 (mt-10) REVERT: H 146 ASP cc_start: 0.8135 (t70) cc_final: 0.7403 (p0) REVERT: H 169 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8000 (mt-10) REVERT: H 175 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8263 (tm-30) REVERT: H 264 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8413 (mmtm) REVERT: I 1 MET cc_start: 0.8697 (mtp) cc_final: 0.8423 (mtm) REVERT: I 2 GLU cc_start: 0.8892 (mp0) cc_final: 0.7702 (mp0) REVERT: I 45 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7823 (mm-30) REVERT: I 65 THR cc_start: 0.8850 (p) cc_final: 0.8589 (p) REVERT: I 67 GLU cc_start: 0.8185 (pm20) cc_final: 0.7935 (pm20) REVERT: J 27 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7967 (mp0) REVERT: J 31 ASP cc_start: 0.8199 (p0) cc_final: 0.7878 (p0) REVERT: J 50 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8676 (mmtm) REVERT: J 52 ASP cc_start: 0.8682 (t0) cc_final: 0.8433 (t0) REVERT: J 55 GLN cc_start: 0.8863 (tt0) cc_final: 0.8650 (tt0) REVERT: K 11 ASP cc_start: 0.8331 (m-30) cc_final: 0.8039 (m-30) REVERT: K 132 ASP cc_start: 0.8261 (t0) cc_final: 0.8049 (t0) REVERT: L 50 GLU cc_start: 0.8747 (pm20) cc_final: 0.8470 (pm20) REVERT: L 146 ASP cc_start: 0.8142 (t70) cc_final: 0.7364 (p0) REVERT: L 169 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7981 (mt-10) REVERT: L 175 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8230 (tm-30) REVERT: L 264 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8544 (mptp) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 1.6858 time to fit residues: 655.4997 Evaluate side-chains 255 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 201 GLN ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN C 349 HIS ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN C 531 GLN D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN D 247 GLN G 201 GLN G 299 ASN G 349 HIS ** G 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 ASN H 22 HIS H 185 GLN H 247 GLN J 55 GLN J 75 GLN K 201 GLN ** K 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 HIS K 499 ASN K 521 GLN L 22 HIS L 161 HIS L 185 GLN L 247 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.054171 restraints weight = 51126.406| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.76 r_work: 0.2600 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24078 Z= 0.201 Angle : 0.578 8.305 32787 Z= 0.293 Chirality : 0.045 0.166 3765 Planarity : 0.004 0.039 4296 Dihedral : 4.351 39.447 3318 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.05 % Allowed : 6.48 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3075 helix: 1.81 (0.20), residues: 753 sheet: 0.01 (0.19), residues: 738 loop : -0.34 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 145 HIS 0.005 0.001 HIS G 472 PHE 0.009 0.001 PHE C 565 TYR 0.010 0.001 TYR H 55 ARG 0.004 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 934) hydrogen bonds : angle 5.69543 ( 2577) covalent geometry : bond 0.00460 (24078) covalent geometry : angle 0.57813 (32787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 2.930 Fit side-chains REVERT: B 9 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8720 (ptmm) REVERT: B 27 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7691 (mp0) REVERT: B 31 ASP cc_start: 0.8586 (p0) cc_final: 0.8309 (p0) REVERT: B 52 ASP cc_start: 0.8664 (t0) cc_final: 0.8033 (t0) REVERT: B 55 GLN cc_start: 0.9103 (tt0) cc_final: 0.8693 (tt0) REVERT: B 78 GLU cc_start: 0.8788 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 11 ASP cc_start: 0.8735 (m-30) cc_final: 0.8411 (m-30) REVERT: D 146 ASP cc_start: 0.8308 (t70) cc_final: 0.7874 (t0) REVERT: D 175 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8396 (tm-30) REVERT: E 2 GLU cc_start: 0.8957 (mp0) cc_final: 0.7851 (mp0) REVERT: F 27 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7859 (mp0) REVERT: F 31 ASP cc_start: 0.8637 (p0) cc_final: 0.8297 (p0) REVERT: F 52 ASP cc_start: 0.8729 (t0) cc_final: 0.8477 (t0) REVERT: F 55 GLN cc_start: 0.9096 (tt0) cc_final: 0.8786 (tt0) REVERT: F 80 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8219 (mm-30) REVERT: G 11 ASP cc_start: 0.8752 (m-30) cc_final: 0.8462 (m-30) REVERT: G 117 GLU cc_start: 0.8429 (tp30) cc_final: 0.7996 (tp30) REVERT: H 146 ASP cc_start: 0.8293 (t70) cc_final: 0.7420 (p0) REVERT: H 175 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8331 (tm-30) REVERT: I 65 THR cc_start: 0.8745 (p) cc_final: 0.8482 (p) REVERT: I 67 GLU cc_start: 0.8664 (pm20) cc_final: 0.8326 (pm20) REVERT: J 27 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7820 (mp0) REVERT: J 31 ASP cc_start: 0.8575 (p0) cc_final: 0.8263 (p0) REVERT: J 52 ASP cc_start: 0.8664 (t0) cc_final: 0.8364 (t0) REVERT: J 55 GLN cc_start: 0.9134 (tt0) cc_final: 0.8827 (tt0) REVERT: J 80 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: K 11 ASP cc_start: 0.8696 (m-30) cc_final: 0.8311 (m-30) REVERT: L 146 ASP cc_start: 0.8260 (t70) cc_final: 0.7395 (p0) REVERT: L 175 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8166 (tm-30) outliers start: 26 outliers final: 6 residues processed: 270 average time/residue: 1.5174 time to fit residues: 464.9698 Evaluate side-chains 264 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 255 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 22 HIS Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 184 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 147 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 230 optimal weight: 8.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN F 75 GLN G 384 GLN H 247 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 299 ASN L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.071147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.055102 restraints weight = 50785.265| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.75 r_work: 0.2620 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24078 Z= 0.145 Angle : 0.540 8.159 32787 Z= 0.273 Chirality : 0.044 0.163 3765 Planarity : 0.004 0.037 4296 Dihedral : 4.290 40.712 3318 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.13 % Allowed : 8.13 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3075 helix: 1.78 (0.20), residues: 759 sheet: -0.09 (0.19), residues: 732 loop : -0.32 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 145 HIS 0.012 0.001 HIS H 22 PHE 0.010 0.001 PHE H 21 TYR 0.009 0.001 TYR K 176 ARG 0.003 0.000 ARG D 258 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 934) hydrogen bonds : angle 5.30876 ( 2577) covalent geometry : bond 0.00330 (24078) covalent geometry : angle 0.54003 (32787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 2.913 Fit side-chains REVERT: B 9 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8741 (ptmm) REVERT: B 23 ARG cc_start: 0.8980 (mtp85) cc_final: 0.8363 (mtp85) REVERT: B 27 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7705 (mp0) REVERT: B 31 ASP cc_start: 0.8575 (p0) cc_final: 0.8322 (p0) REVERT: B 52 ASP cc_start: 0.8685 (t0) cc_final: 0.8343 (t0) REVERT: B 55 GLN cc_start: 0.9095 (tt0) cc_final: 0.8756 (tt0) REVERT: B 78 GLU cc_start: 0.8768 (tt0) cc_final: 0.8224 (tm-30) REVERT: C 11 ASP cc_start: 0.8728 (m-30) cc_final: 0.8396 (m-30) REVERT: C 117 GLU cc_start: 0.8432 (tp30) cc_final: 0.8088 (tp30) REVERT: C 334 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7182 (tp30) REVERT: D 146 ASP cc_start: 0.8279 (t70) cc_final: 0.7879 (t0) REVERT: D 175 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8378 (tm-30) REVERT: E 2 GLU cc_start: 0.8983 (mp0) cc_final: 0.7877 (mp0) REVERT: F 27 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7853 (mp0) REVERT: F 31 ASP cc_start: 0.8607 (p0) cc_final: 0.8302 (p0) REVERT: F 52 ASP cc_start: 0.8709 (t0) cc_final: 0.8372 (t0) REVERT: F 55 GLN cc_start: 0.9109 (tt0) cc_final: 0.8763 (tt0) REVERT: F 80 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8247 (mm-30) REVERT: G 11 ASP cc_start: 0.8723 (m-30) cc_final: 0.8423 (m-30) REVERT: G 117 GLU cc_start: 0.8409 (tp30) cc_final: 0.7940 (tp30) REVERT: H 146 ASP cc_start: 0.8251 (t70) cc_final: 0.7422 (p0) REVERT: H 175 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8406 (tm-30) REVERT: I 2 GLU cc_start: 0.9064 (mp0) cc_final: 0.7848 (mp0) REVERT: I 65 THR cc_start: 0.8726 (p) cc_final: 0.8482 (p) REVERT: I 67 GLU cc_start: 0.8668 (pm20) cc_final: 0.8329 (pm20) REVERT: J 27 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7782 (mp0) REVERT: J 31 ASP cc_start: 0.8539 (p0) cc_final: 0.8219 (p0) REVERT: J 52 ASP cc_start: 0.8660 (t0) cc_final: 0.8313 (t0) REVERT: J 55 GLN cc_start: 0.9164 (tt0) cc_final: 0.8848 (tt0) REVERT: J 80 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: K 11 ASP cc_start: 0.8715 (m-30) cc_final: 0.8320 (m-30) REVERT: L 146 ASP cc_start: 0.8200 (t70) cc_final: 0.7386 (p0) REVERT: L 175 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8270 (tm-30) outliers start: 28 outliers final: 9 residues processed: 285 average time/residue: 2.0958 time to fit residues: 682.4515 Evaluate side-chains 276 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain L residue 27 LYS Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.055740 restraints weight = 51092.566| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.78 r_work: 0.2637 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24078 Z= 0.122 Angle : 0.524 7.637 32787 Z= 0.265 Chirality : 0.044 0.161 3765 Planarity : 0.004 0.036 4296 Dihedral : 4.214 40.746 3318 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.89 % Allowed : 9.66 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3075 helix: 1.81 (0.20), residues: 759 sheet: -0.03 (0.19), residues: 729 loop : -0.34 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 145 HIS 0.007 0.001 HIS L 161 PHE 0.006 0.001 PHE G 565 TYR 0.009 0.001 TYR K 176 ARG 0.002 0.000 ARG J 23 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 934) hydrogen bonds : angle 5.09670 ( 2577) covalent geometry : bond 0.00278 (24078) covalent geometry : angle 0.52393 (32787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 263 time to evaluate : 2.647 Fit side-chains REVERT: B 9 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8744 (ptmm) REVERT: B 27 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7718 (mp0) REVERT: B 31 ASP cc_start: 0.8553 (p0) cc_final: 0.8311 (p0) REVERT: B 52 ASP cc_start: 0.8652 (t0) cc_final: 0.8319 (t0) REVERT: B 55 GLN cc_start: 0.9097 (tt0) cc_final: 0.8753 (tt0) REVERT: B 78 GLU cc_start: 0.8766 (tt0) cc_final: 0.8175 (tm-30) REVERT: C 11 ASP cc_start: 0.8720 (m-30) cc_final: 0.8381 (m-30) REVERT: C 117 GLU cc_start: 0.8416 (tp30) cc_final: 0.8067 (tp30) REVERT: C 334 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7225 (tp30) REVERT: D 146 ASP cc_start: 0.8246 (t70) cc_final: 0.7346 (p0) REVERT: D 175 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8392 (tm-30) REVERT: F 27 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7863 (mp0) REVERT: F 31 ASP cc_start: 0.8581 (p0) cc_final: 0.8287 (p0) REVERT: F 52 ASP cc_start: 0.8691 (t0) cc_final: 0.8292 (t0) REVERT: F 55 GLN cc_start: 0.9118 (tt0) cc_final: 0.8773 (tt0) REVERT: F 80 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: G 11 ASP cc_start: 0.8735 (m-30) cc_final: 0.8427 (m-30) REVERT: G 117 GLU cc_start: 0.8404 (tp30) cc_final: 0.7918 (tp30) REVERT: H 146 ASP cc_start: 0.8243 (t70) cc_final: 0.7414 (p0) REVERT: H 175 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8381 (tm-30) REVERT: I 2 GLU cc_start: 0.9054 (mp0) cc_final: 0.7828 (mp0) REVERT: I 65 THR cc_start: 0.8706 (p) cc_final: 0.8441 (p) REVERT: I 67 GLU cc_start: 0.8682 (pm20) cc_final: 0.8344 (pm20) REVERT: J 27 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7737 (mp0) REVERT: J 31 ASP cc_start: 0.8520 (p0) cc_final: 0.8213 (p0) REVERT: J 52 ASP cc_start: 0.8605 (t0) cc_final: 0.8314 (t0) REVERT: J 55 GLN cc_start: 0.9148 (tt0) cc_final: 0.8813 (tt0) REVERT: J 80 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8228 (mm-30) REVERT: K 11 ASP cc_start: 0.8709 (m-30) cc_final: 0.8314 (m-30) REVERT: L 146 ASP cc_start: 0.8229 (t70) cc_final: 0.7429 (p0) REVERT: L 175 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8283 (tm-30) outliers start: 22 outliers final: 7 residues processed: 269 average time/residue: 1.4930 time to fit residues: 457.4137 Evaluate side-chains 278 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 268 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 82 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 286 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN B 54 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN F 12 GLN G 531 GLN H 22 HIS H 161 HIS H 247 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 531 GLN L 22 HIS L 247 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.067466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.051253 restraints weight = 52162.357| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.76 r_work: 0.2521 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 24078 Z= 0.408 Angle : 0.684 8.326 32787 Z= 0.342 Chirality : 0.049 0.186 3765 Planarity : 0.005 0.042 4296 Dihedral : 4.648 41.198 3318 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.29 % Allowed : 10.63 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3075 helix: 1.55 (0.20), residues: 756 sheet: 0.04 (0.19), residues: 723 loop : -0.37 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 145 HIS 0.008 0.001 HIS C 320 PHE 0.026 0.002 PHE H 238 TYR 0.019 0.002 TYR K 176 ARG 0.004 0.001 ARG F 77 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 934) hydrogen bonds : angle 5.43953 ( 2577) covalent geometry : bond 0.00938 (24078) covalent geometry : angle 0.68353 (32787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 2.689 Fit side-chains REVERT: B 9 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8728 (ptmm) REVERT: B 27 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7798 (mp0) REVERT: B 31 ASP cc_start: 0.8590 (p0) cc_final: 0.8350 (p0) REVERT: B 52 ASP cc_start: 0.8735 (t0) cc_final: 0.8077 (t0) REVERT: B 55 GLN cc_start: 0.9066 (tt0) cc_final: 0.8561 (tt0) REVERT: C 11 ASP cc_start: 0.8723 (m-30) cc_final: 0.8356 (m-30) REVERT: C 117 GLU cc_start: 0.8493 (tp30) cc_final: 0.8016 (tp30) REVERT: D 146 ASP cc_start: 0.8426 (t70) cc_final: 0.8071 (t0) REVERT: D 175 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8476 (tm-30) REVERT: E 2 GLU cc_start: 0.9061 (mp0) cc_final: 0.8000 (mp0) REVERT: F 27 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7859 (mp0) REVERT: F 31 ASP cc_start: 0.8607 (p0) cc_final: 0.8396 (p0) REVERT: F 52 ASP cc_start: 0.8782 (t0) cc_final: 0.8411 (t0) REVERT: F 55 GLN cc_start: 0.9088 (tt0) cc_final: 0.8737 (tt0) REVERT: F 80 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8246 (mm-30) REVERT: G 11 ASP cc_start: 0.8718 (m-30) cc_final: 0.8434 (m-30) REVERT: G 117 GLU cc_start: 0.8429 (tp30) cc_final: 0.7954 (tp30) REVERT: H 90 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8716 (mtmt) REVERT: H 146 ASP cc_start: 0.8345 (t70) cc_final: 0.7961 (t0) REVERT: H 175 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8466 (tm-30) REVERT: I 2 GLU cc_start: 0.9105 (mp0) cc_final: 0.7909 (mp0) REVERT: J 27 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8006 (mp0) REVERT: J 31 ASP cc_start: 0.8515 (p0) cc_final: 0.8282 (p0) REVERT: J 52 ASP cc_start: 0.8694 (t0) cc_final: 0.8362 (t0) REVERT: J 55 GLN cc_start: 0.9134 (tt0) cc_final: 0.8823 (tt0) REVERT: J 80 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: K 11 ASP cc_start: 0.8692 (m-30) cc_final: 0.8317 (m-30) REVERT: L 146 ASP cc_start: 0.8427 (t70) cc_final: 0.8086 (t0) REVERT: L 175 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8537 (tm-30) outliers start: 32 outliers final: 9 residues processed: 263 average time/residue: 1.5764 time to fit residues: 468.6357 Evaluate side-chains 272 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 79 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 132 optimal weight: 0.0040 chunk 85 optimal weight: 5.9990 chunk 117 optimal weight: 0.0270 chunk 136 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 161 HIS I 97 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 384 GLN L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.055845 restraints weight = 50402.174| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.75 r_work: 0.2640 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24078 Z= 0.109 Angle : 0.539 8.185 32787 Z= 0.273 Chirality : 0.044 0.167 3765 Planarity : 0.004 0.037 4296 Dihedral : 4.302 40.617 3318 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.13 % Allowed : 11.39 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3075 helix: 1.76 (0.20), residues: 753 sheet: 0.15 (0.19), residues: 678 loop : -0.39 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 435 HIS 0.005 0.001 HIS L 161 PHE 0.024 0.001 PHE H 238 TYR 0.008 0.001 TYR D 204 ARG 0.002 0.000 ARG K 52 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 934) hydrogen bonds : angle 4.95573 ( 2577) covalent geometry : bond 0.00244 (24078) covalent geometry : angle 0.53932 (32787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 2.646 Fit side-chains REVERT: A 2 GLU cc_start: 0.9025 (mp0) cc_final: 0.8060 (mp0) REVERT: A 10 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8367 (mmmt) REVERT: B 9 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8706 (ptmm) REVERT: B 27 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7740 (mp0) REVERT: B 31 ASP cc_start: 0.8534 (p0) cc_final: 0.8316 (p0) REVERT: B 52 ASP cc_start: 0.8622 (t0) cc_final: 0.8278 (t0) REVERT: B 55 GLN cc_start: 0.9083 (tt0) cc_final: 0.8586 (tt0) REVERT: B 78 GLU cc_start: 0.8765 (tt0) cc_final: 0.8081 (tm-30) REVERT: B 80 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8173 (tp30) REVERT: C 11 ASP cc_start: 0.8722 (m-30) cc_final: 0.8383 (m-30) REVERT: C 117 GLU cc_start: 0.8475 (tp30) cc_final: 0.7952 (tp30) REVERT: D 146 ASP cc_start: 0.8273 (t70) cc_final: 0.7920 (t0) REVERT: D 175 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8386 (tm-30) REVERT: F 27 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7833 (mp0) REVERT: F 31 ASP cc_start: 0.8541 (p0) cc_final: 0.8286 (p0) REVERT: F 52 ASP cc_start: 0.8673 (t0) cc_final: 0.8256 (t0) REVERT: F 55 GLN cc_start: 0.9093 (tt0) cc_final: 0.8712 (tt0) REVERT: F 80 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8129 (mm-30) REVERT: G 11 ASP cc_start: 0.8740 (m-30) cc_final: 0.8432 (m-30) REVERT: G 117 GLU cc_start: 0.8417 (tp30) cc_final: 0.7959 (tp30) REVERT: H 146 ASP cc_start: 0.8236 (t70) cc_final: 0.7409 (p0) REVERT: H 175 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8376 (tm-30) REVERT: I 2 GLU cc_start: 0.9054 (mp0) cc_final: 0.7819 (mp0) REVERT: I 58 GLU cc_start: 0.8737 (tp30) cc_final: 0.8519 (tp30) REVERT: J 27 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7806 (mp0) REVERT: J 31 ASP cc_start: 0.8468 (p0) cc_final: 0.8194 (p0) REVERT: J 52 ASP cc_start: 0.8573 (t0) cc_final: 0.8267 (t0) REVERT: J 55 GLN cc_start: 0.9121 (tt0) cc_final: 0.8790 (tt0) REVERT: J 80 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8294 (mm-30) REVERT: K 11 ASP cc_start: 0.8702 (m-30) cc_final: 0.8300 (m-30) REVERT: K 117 GLU cc_start: 0.8541 (tp30) cc_final: 0.8325 (tp30) REVERT: L 146 ASP cc_start: 0.8282 (t70) cc_final: 0.7474 (p0) REVERT: L 175 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8359 (tm-30) outliers start: 28 outliers final: 8 residues processed: 289 average time/residue: 1.5503 time to fit residues: 509.4874 Evaluate side-chains 267 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 31 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 236 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 161 HIS H 247 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 ASN L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.055458 restraints weight = 51133.906| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.77 r_work: 0.2630 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24078 Z= 0.132 Angle : 0.539 7.969 32787 Z= 0.271 Chirality : 0.044 0.182 3765 Planarity : 0.004 0.037 4296 Dihedral : 4.221 40.301 3318 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.97 % Allowed : 12.12 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3075 helix: 1.82 (0.20), residues: 756 sheet: 0.30 (0.19), residues: 678 loop : -0.44 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 145 HIS 0.006 0.001 HIS L 161 PHE 0.022 0.001 PHE H 238 TYR 0.010 0.001 TYR H 92 ARG 0.003 0.000 ARG K 52 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 934) hydrogen bonds : angle 4.92075 ( 2577) covalent geometry : bond 0.00303 (24078) covalent geometry : angle 0.53860 (32787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 2.789 Fit side-chains REVERT: B 27 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7754 (mp0) REVERT: B 31 ASP cc_start: 0.8545 (p0) cc_final: 0.8339 (p0) REVERT: B 52 ASP cc_start: 0.8651 (t0) cc_final: 0.8286 (t0) REVERT: B 55 GLN cc_start: 0.9088 (tt0) cc_final: 0.8737 (tt0) REVERT: B 78 GLU cc_start: 0.8765 (tt0) cc_final: 0.8100 (tm-30) REVERT: C 11 ASP cc_start: 0.8717 (m-30) cc_final: 0.8383 (m-30) REVERT: C 117 GLU cc_start: 0.8463 (tp30) cc_final: 0.7982 (tp30) REVERT: D 146 ASP cc_start: 0.8260 (t70) cc_final: 0.7907 (t0) REVERT: D 175 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8369 (tm-30) REVERT: F 27 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7832 (mp0) REVERT: F 31 ASP cc_start: 0.8542 (p0) cc_final: 0.8305 (p0) REVERT: F 52 ASP cc_start: 0.8722 (t0) cc_final: 0.8292 (t0) REVERT: F 55 GLN cc_start: 0.9110 (tt0) cc_final: 0.8736 (tt0) REVERT: F 80 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8329 (mm-30) REVERT: G 11 ASP cc_start: 0.8734 (m-30) cc_final: 0.8433 (m-30) REVERT: G 117 GLU cc_start: 0.8393 (tp30) cc_final: 0.7938 (tp30) REVERT: H 146 ASP cc_start: 0.8234 (t70) cc_final: 0.7399 (p0) REVERT: H 175 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8410 (tm-30) REVERT: I 2 GLU cc_start: 0.9052 (mp0) cc_final: 0.7808 (mp0) REVERT: J 27 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7806 (mp0) REVERT: J 31 ASP cc_start: 0.8470 (p0) cc_final: 0.8205 (p0) REVERT: J 52 ASP cc_start: 0.8581 (t0) cc_final: 0.8254 (t0) REVERT: J 55 GLN cc_start: 0.9115 (tt0) cc_final: 0.8776 (tt0) REVERT: J 78 GLU cc_start: 0.8879 (tt0) cc_final: 0.8171 (tm-30) REVERT: J 80 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: K 11 ASP cc_start: 0.8703 (m-30) cc_final: 0.8308 (m-30) REVERT: K 60 MET cc_start: 0.9095 (pmm) cc_final: 0.8845 (pmm) REVERT: K 117 GLU cc_start: 0.8542 (tp30) cc_final: 0.8302 (tp30) REVERT: L 146 ASP cc_start: 0.8304 (t70) cc_final: 0.7486 (p0) REVERT: L 175 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8327 (tm-30) outliers start: 24 outliers final: 6 residues processed: 272 average time/residue: 1.4574 time to fit residues: 452.0805 Evaluate side-chains 275 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 295 optimal weight: 9.9990 chunk 169 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 31 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 161 HIS ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.055506 restraints weight = 50781.563| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.76 r_work: 0.2632 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24078 Z= 0.140 Angle : 0.548 9.770 32787 Z= 0.275 Chirality : 0.044 0.184 3765 Planarity : 0.004 0.036 4296 Dihedral : 4.201 40.289 3318 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.93 % Allowed : 12.72 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3075 helix: 1.68 (0.20), residues: 774 sheet: 0.35 (0.19), residues: 675 loop : -0.44 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 145 HIS 0.005 0.001 HIS D 22 PHE 0.021 0.001 PHE H 238 TYR 0.012 0.001 TYR K 176 ARG 0.002 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 934) hydrogen bonds : angle 4.88609 ( 2577) covalent geometry : bond 0.00326 (24078) covalent geometry : angle 0.54809 (32787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 2.847 Fit side-chains REVERT: A 2 GLU cc_start: 0.9042 (mp0) cc_final: 0.8051 (mp0) REVERT: A 58 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8452 (tp30) REVERT: B 27 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7734 (mp0) REVERT: B 52 ASP cc_start: 0.8582 (t0) cc_final: 0.8246 (t0) REVERT: B 55 GLN cc_start: 0.9086 (tt0) cc_final: 0.8726 (tt0) REVERT: B 78 GLU cc_start: 0.8751 (tt0) cc_final: 0.8095 (tm-30) REVERT: B 80 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8256 (tp30) REVERT: C 11 ASP cc_start: 0.8716 (m-30) cc_final: 0.8381 (m-30) REVERT: C 117 GLU cc_start: 0.8464 (tp30) cc_final: 0.7973 (tp30) REVERT: D 146 ASP cc_start: 0.8260 (t70) cc_final: 0.7919 (t0) REVERT: D 175 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8403 (tm-30) REVERT: F 27 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7868 (mp0) REVERT: F 31 ASP cc_start: 0.8529 (p0) cc_final: 0.8294 (p0) REVERT: F 52 ASP cc_start: 0.8698 (t0) cc_final: 0.8263 (t0) REVERT: F 55 GLN cc_start: 0.9113 (tt0) cc_final: 0.8726 (tt0) REVERT: F 80 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8264 (mm-30) REVERT: G 11 ASP cc_start: 0.8721 (m-30) cc_final: 0.8424 (m-30) REVERT: G 117 GLU cc_start: 0.8360 (tp30) cc_final: 0.7914 (tp30) REVERT: H 146 ASP cc_start: 0.8245 (t70) cc_final: 0.7434 (p0) REVERT: H 175 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8387 (tm-30) REVERT: H 264 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8822 (mtpt) REVERT: I 2 GLU cc_start: 0.9052 (mp0) cc_final: 0.7807 (mp0) REVERT: J 27 GLU cc_start: 0.8508 (mt-10) cc_final: 0.7805 (mp0) REVERT: J 31 ASP cc_start: 0.8468 (p0) cc_final: 0.8206 (p0) REVERT: J 52 ASP cc_start: 0.8582 (t0) cc_final: 0.8273 (t0) REVERT: J 55 GLN cc_start: 0.9122 (tt0) cc_final: 0.8786 (tt0) REVERT: J 80 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: K 11 ASP cc_start: 0.8695 (m-30) cc_final: 0.8302 (m-30) REVERT: K 117 GLU cc_start: 0.8518 (tp30) cc_final: 0.8212 (tp30) REVERT: L 146 ASP cc_start: 0.8297 (t70) cc_final: 0.7479 (p0) REVERT: L 175 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8333 (tm-30) outliers start: 23 outliers final: 6 residues processed: 281 average time/residue: 1.4698 time to fit residues: 470.1762 Evaluate side-chains 278 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 271 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 267 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 161 HIS ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.055467 restraints weight = 50633.561| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.77 r_work: 0.2630 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24078 Z= 0.144 Angle : 0.555 9.325 32787 Z= 0.277 Chirality : 0.044 0.162 3765 Planarity : 0.004 0.036 4296 Dihedral : 4.196 40.303 3318 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.93 % Allowed : 12.92 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3075 helix: 1.83 (0.20), residues: 756 sheet: 0.30 (0.19), residues: 705 loop : -0.47 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 145 HIS 0.005 0.001 HIS C 134 PHE 0.021 0.001 PHE H 238 TYR 0.013 0.001 TYR K 176 ARG 0.006 0.000 ARG J 23 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 934) hydrogen bonds : angle 4.87035 ( 2577) covalent geometry : bond 0.00335 (24078) covalent geometry : angle 0.55468 (32787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 2.659 Fit side-chains REVERT: A 2 GLU cc_start: 0.9042 (mp0) cc_final: 0.8047 (mp0) REVERT: A 58 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8469 (tp30) REVERT: B 27 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7742 (mp0) REVERT: B 52 ASP cc_start: 0.8628 (t0) cc_final: 0.7937 (t70) REVERT: B 55 GLN cc_start: 0.9096 (tt0) cc_final: 0.8534 (tt0) REVERT: B 80 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8182 (tp30) REVERT: C 11 ASP cc_start: 0.8722 (m-30) cc_final: 0.8386 (m-30) REVERT: C 117 GLU cc_start: 0.8465 (tp30) cc_final: 0.7974 (tp30) REVERT: D 146 ASP cc_start: 0.8264 (t70) cc_final: 0.7921 (t0) REVERT: D 175 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8449 (tm-30) REVERT: F 27 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7877 (mp0) REVERT: F 31 ASP cc_start: 0.8534 (p0) cc_final: 0.8300 (p0) REVERT: F 52 ASP cc_start: 0.8714 (t0) cc_final: 0.8263 (t0) REVERT: F 55 GLN cc_start: 0.9114 (tt0) cc_final: 0.8727 (tt0) REVERT: F 80 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8267 (mm-30) REVERT: G 11 ASP cc_start: 0.8731 (m-30) cc_final: 0.8435 (m-30) REVERT: G 117 GLU cc_start: 0.8369 (tp30) cc_final: 0.7921 (tp30) REVERT: H 146 ASP cc_start: 0.8245 (t70) cc_final: 0.7424 (p0) REVERT: H 175 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8471 (tm-30) REVERT: H 264 LYS cc_start: 0.9052 (mmtp) cc_final: 0.8836 (mtpt) REVERT: I 2 GLU cc_start: 0.9047 (mp0) cc_final: 0.7806 (mp0) REVERT: J 27 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7770 (mp0) REVERT: J 31 ASP cc_start: 0.8462 (p0) cc_final: 0.8200 (p0) REVERT: J 52 ASP cc_start: 0.8579 (t0) cc_final: 0.8264 (t0) REVERT: J 55 GLN cc_start: 0.9129 (tt0) cc_final: 0.8793 (tt0) REVERT: J 78 GLU cc_start: 0.8869 (tt0) cc_final: 0.8129 (tm-30) REVERT: J 80 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8350 (mm-30) REVERT: K 11 ASP cc_start: 0.8698 (m-30) cc_final: 0.8304 (m-30) REVERT: K 117 GLU cc_start: 0.8518 (tp30) cc_final: 0.8224 (tp30) REVERT: L 67 ASP cc_start: 0.8131 (m-30) cc_final: 0.7595 (m-30) REVERT: L 146 ASP cc_start: 0.8302 (t70) cc_final: 0.7487 (p0) REVERT: L 175 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8304 (tm-30) REVERT: L 208 ASP cc_start: 0.8788 (m-30) cc_final: 0.8245 (m-30) outliers start: 23 outliers final: 8 residues processed: 285 average time/residue: 1.4863 time to fit residues: 483.1673 Evaluate side-chains 278 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 269 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 144 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 278 optimal weight: 0.8980 chunk 283 optimal weight: 3.9990 chunk 55 optimal weight: 0.0270 chunk 168 optimal weight: 0.4980 chunk 238 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 247 GLN G 198 ASN G 251 ASN H 22 HIS H 161 HIS ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 198 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS L 247 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.057100 restraints weight = 50651.147| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.78 r_work: 0.2669 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24078 Z= 0.104 Angle : 0.553 9.407 32787 Z= 0.276 Chirality : 0.044 0.196 3765 Planarity : 0.004 0.037 4296 Dihedral : 4.120 40.107 3318 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.76 % Allowed : 13.53 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3075 helix: 1.70 (0.20), residues: 774 sheet: 0.49 (0.19), residues: 660 loop : -0.42 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 435 HIS 0.005 0.001 HIS D 22 PHE 0.020 0.001 PHE H 238 TYR 0.010 0.001 TYR K 176 ARG 0.003 0.000 ARG J 23 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 934) hydrogen bonds : angle 4.77748 ( 2577) covalent geometry : bond 0.00238 (24078) covalent geometry : angle 0.55349 (32787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 288 time to evaluate : 2.805 Fit side-chains REVERT: A 2 GLU cc_start: 0.9009 (mp0) cc_final: 0.8031 (mp0) REVERT: B 27 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7701 (mp0) REVERT: B 52 ASP cc_start: 0.8525 (t0) cc_final: 0.8191 (t0) REVERT: B 55 GLN cc_start: 0.9096 (tt0) cc_final: 0.8605 (tt0) REVERT: B 78 GLU cc_start: 0.8742 (tt0) cc_final: 0.8077 (tm-30) REVERT: B 80 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8240 (tp30) REVERT: B 102 GLU cc_start: 0.7997 (mp0) cc_final: 0.7710 (pm20) REVERT: C 11 ASP cc_start: 0.8720 (m-30) cc_final: 0.8385 (m-30) REVERT: C 117 GLU cc_start: 0.8441 (tp30) cc_final: 0.7951 (tp30) REVERT: D 146 ASP cc_start: 0.8252 (t70) cc_final: 0.7915 (t0) REVERT: D 175 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8484 (tm-30) REVERT: F 27 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7866 (mp0) REVERT: F 31 ASP cc_start: 0.8504 (p0) cc_final: 0.8262 (p0) REVERT: F 52 ASP cc_start: 0.8707 (t0) cc_final: 0.8277 (t0) REVERT: F 55 GLN cc_start: 0.9133 (tt0) cc_final: 0.8757 (tt0) REVERT: F 80 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8224 (mm-30) REVERT: G 11 ASP cc_start: 0.8719 (m-30) cc_final: 0.8410 (m-30) REVERT: G 117 GLU cc_start: 0.8356 (tp30) cc_final: 0.7912 (tp30) REVERT: G 144 GLU cc_start: 0.8552 (tt0) cc_final: 0.8022 (tm-30) REVERT: H 146 ASP cc_start: 0.8216 (t70) cc_final: 0.7414 (p0) REVERT: H 175 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8406 (tm-30) REVERT: H 264 LYS cc_start: 0.9071 (mmtp) cc_final: 0.8868 (mtpt) REVERT: I 2 GLU cc_start: 0.9032 (mp0) cc_final: 0.7778 (mp0) REVERT: J 9 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8921 (ptmt) REVERT: J 27 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7728 (mp0) REVERT: J 31 ASP cc_start: 0.8453 (p0) cc_final: 0.8180 (p0) REVERT: J 52 ASP cc_start: 0.8559 (t0) cc_final: 0.8233 (t0) REVERT: J 55 GLN cc_start: 0.9136 (tt0) cc_final: 0.8798 (tt0) REVERT: J 78 GLU cc_start: 0.8848 (tt0) cc_final: 0.8130 (tm-30) REVERT: J 80 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8332 (mm-30) REVERT: K 11 ASP cc_start: 0.8707 (m-30) cc_final: 0.8312 (m-30) REVERT: K 117 GLU cc_start: 0.8522 (tp30) cc_final: 0.8256 (tp30) REVERT: L 67 ASP cc_start: 0.8103 (m-30) cc_final: 0.7568 (m-30) REVERT: L 146 ASP cc_start: 0.8256 (t70) cc_final: 0.7478 (p0) REVERT: L 175 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8302 (tm-30) outliers start: 19 outliers final: 6 residues processed: 299 average time/residue: 1.4782 time to fit residues: 504.1668 Evaluate side-chains 277 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 269 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 9 LYS Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 172 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 247 GLN H 22 HIS H 161 HIS ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.056105 restraints weight = 50592.393| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.76 r_work: 0.2646 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24078 Z= 0.143 Angle : 0.570 10.343 32787 Z= 0.282 Chirality : 0.044 0.193 3765 Planarity : 0.004 0.036 4296 Dihedral : 4.149 40.138 3318 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.76 % Allowed : 14.01 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3075 helix: 1.76 (0.20), residues: 771 sheet: 0.54 (0.19), residues: 645 loop : -0.38 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 145 HIS 0.005 0.001 HIS H 22 PHE 0.019 0.001 PHE H 238 TYR 0.010 0.001 TYR K 176 ARG 0.004 0.000 ARG J 23 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 934) hydrogen bonds : angle 4.82930 ( 2577) covalent geometry : bond 0.00333 (24078) covalent geometry : angle 0.57019 (32787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14844.95 seconds wall clock time: 256 minutes 21.31 seconds (15381.31 seconds total)